After spending the summer with his mother in Philadelphia, Dawson returns to Capeside and meets a beautiful, outgoing, young woman, named Eve, on the bus from Philadelphia. Eve soon brings trouble to Dawson's ho-hum life when he accidentally wrecks his father's boat during an outing with her and tries to come up with $3,000 to repair it before Mitch finds out. So, Eve helps out by throwing a rave party at the Leery house with strippers from the club she works at. Meanwhile, Joey, who has frozen Dawson out all summer for forcing her to rat out her father, realizes that she still has feelings for him again when they meet during the first day back at Capeside High as juniors. While working at the Capeside Marina, Joey deals with the come-ons from her sexist boss Rob Logan. Jen gets more than she bargained for when she tries out for Capeside High's cheer leading squad and faces off in a war-of-wits against the mean-spirited head cheerleader, and acquires her position. Also, Mitch gets a new job as Capeside High's varsity football coach, and a new charismatic, but very stern, principal, named Howard Green, arrives to administrate the school.

Dawson is recruited by Mitch and Principal Green to produce a film for the football pep rally, while the mysterious Eve continues to temp Dawson. Meanwhile, Pacey enlists Joey's help for help in bringing Andie back to Capeside. But Pacey's and Andie's long-awaited reunion doesn't go exactly as Pacey intended when a guilt-ridden Andie tells him about a fling she had of her own and as a result, Pacey breaks up with her. Also, Jack is asked to join the football team, the Capeside Minutemen, and then comes to an unexpected understanding with his father who has returned to Capeside after moving his struggling business to live near Jack and Andie. Also, head cheerleader Jen has a meeting of minds with the new Capeside quarterback; the rookie freshman Henry Parker.

Dawson is stunned when Eve presents him with stolen copies of the school's PSAT's and everyone is tempted to cheat, including Joey whose scholarship to Harvard is dependent on her SAT scores. But when the test goes missing, Dawson wonders who stole it and accusations run high, especially with Pacey. Meanwhile, Jack feels that the whole football team is verbally and physically beating down on him because he is gay, while Henry Parker asks Jack for advice on talking to Jen. Also, Rob Logan continues to make Joey's life difficult at work after she turns down an offer to go on a date with him.

Mitch and Dawson are at odds with each other again when Dawson moves forward with a news piece for his mother's Philadelphia station using Mitch's star player, Jack, as his subject matter, even though Mitch is vehemently opposed to it. Meanwhile, Joey and Pacey find themselves in cahoots when they must pay the price for ditching school for the day so Pacey can work on a 'dream boat' he plans to sail around the world in, while Andie panics and jumps to conclusions when Principal Green wants to meet with her after school after mistakenly thinking that he knows about her cheating on the PSAT's. Also, Jen goes to great lengths to remove herself as head cheerleader due to the stress of being in that position, but is shocked at the end results which involve the painfully shy Henry Parker.

During a late-summer heat wave, Dawson plays detective when Eve's mysterious ways, including breaking and entering at Grams house, cause him to wonder about her reasons for being in Capeside and he gets Pacey to help him. But Eve is too slick for Dawson's inept detective ways and throws him off balance every time. Meanwhile, Joey's misgivings of Rob lead her to crash his date with Andie at the movies which leads to him firing her. Also, Jack goes against Jen's wishes and sets her up for a rendezvous with Henry.

Nominated for Capeside's Homecoming Queen, Jen wins and is put in charge of planning the Annual Homecoming Queen Gala, where she shocks the prim-and-proper committee president, Constance Freckling, and the entire town with the entertainment, while Jen also asks the painfully sky Henry to be her date. After Joey and Pacey save Andie from the libidos Rob, she wants to get back together with Pacey. But Joey becomes suspicious that Andie may have orchestrated the event to make Pacey her savior. Meanwhile, Dawson is distressed with his mother, Gail, unexpectedly returns from Philadelphia, and soon learns that she was fired from her job, while he is torn about telling Jen the scandalous secret he has about the departed Eve.

Dawson recruits Joey, Pacey and Jen to be his guerrilla crew on a documentary for history class about Witch Island, a local spot shrouded in mystery for its reputation for being haunted by witches. During their work, they are haunted by tall tales of witches and love lost that has Dawson and Joey questioning their failed romance and Jen and Pacey on considering a new kind of friendship. Back at school, Andie takes her new job on Capeside's disciplinary committee a little too seriously when she tries taking back the halls of the outgoing students.

When Jen's estranged mother, Helen, unexpectedly arrives in Capeside on Thanksgiving morning, Dawson confronts her about her secret past involving Eve, and makes a decision to help bridge the gap between Jen and Helen Lindley during the dinner at the Leery house where Grams takes over the cooking munch to Gail's chagrin. Meanwhile, Jen continues to pursue a new type of friendship with Pacey. Mitch and Gail make known to Dawson the future of the Leery family. Joey, Bessie and baby Alexander join the Leerys for Thanksgiving after their turkey dinner literally falls through. Also, Jack and Andie end up attending the Thanksgiving feast at the Leery house after being left alone by their father for the day, and Pacey soon follows suit after apparently being unable to stand Thanksgiving at his house with his crude, crass, and drunkard parents which makes both him and Andie uncomfortable with each others presence.

Dawson becomes suspicious of Pacey's awkward behavior and misconstrues his actions when he learns that Pacey has been spending time with Joey. As it turns out, Joey has asked Pacey to be her ballroom dance partner in exchange for tutoring him in math. Meanwhile, Pacey begins to doubt about moving forward his secret, no-strings-attached, relationship of sex with Jen. Also, Andie urges Jack to meet a gay student from a nearby town who contacted him via the Internet after seeing Dawson's news story.

Dawson, Joey, Jack and Andie spend the weekend at Boston University for an advanced look at college and where Dawson has entered his Witch Island documentary in a student film festival. But he finds the reception not to his liking along with recommendations from Nikki Green, an aspiring student director of her own. Elsewhere on the campus, due to a clerical error, Joey's weekend guide is not what she expected as it turns out to be a guy, named A.J. Moller, who shares her love of the same literature. Meanwhile, Andie's pursuit for an advanced admissions interview leads her to some inspirational advice from an unlikely source: a career secretary. Also, Jack takes a risk and explores the local gay community.

Dawson experiences an identity crisis when Nikki, who happens to be Principal Green's daughter, arrives in Capeside and gives Dawson advice on his future as an aspiring young director like her. Joey experiences her own crisis when Dawson won't open up to her about the pain of his parents divorce. Meanwhile, during a weekend outdoor folk concert, Jack's first efforts to hit on another guy are rebuffed when the man, Ethan, only wants to be friends. Elsewhere in the camp, Jen realizes that she may have passed up the chance at something special with Henry. Also, Pacey and Andie uncomfortably find themselves sharing the same after school activity of planning a school play of 'Barefoot in the Park,' with Pacey in the lead role, and Andie as the assistant director.

Joey's friends and their families work together to make sure that the opening of Potter's Bed & Breakfast is a success and that she and Bessie don't lose everything they have after Pacey surprises them with a visit from a prestigious travel critic. Meanwhile, Jen admits her concerns to Grams about getting close to Henry. Jack considers moving back home to his own house after hearing Andie's loving plea. Also, Dawson tries to understand the connection between his parents after their divorce.

Dawson makes the radical move of dropping out of film class to spend some time re-evaluating his teenage years against Nikki's advice. Meanwhile, Joey is torn between attending Pacey's opening night and her date with A.J., who has come to Capeside for the day. Before opening night of the school play of 'Barefoot in the Park', Andie must take over as director when the faculty director, Mr. Broderick, becomes ill and she tries to persuade Pacey to act out his feelings when he gets stage fright. Also, Jen agrees to go out on a date with Henry by taking him out to see the play. But she throws him another block by bringing Grams with her.

Joey questions Dawson's state of mind when he and Pacey decide to lead her and their friends to a secret location party on a golf course hosted by Matt Caulfield, a wealthy and snobbish student connected to a clique of spoiled rich kids from school, infamous for their complete and utter debauchery. Meanwhile, Jack's ex-girlfriend, Kate Douglas, arrives from Rhode Island for a visit while nursing a broken heart, but is unaware of Jack's coming out. Also, Jen's first date with Henry is a Valentine's Day she won't soon forget when he passes out after donating four pints of blood to pay for their romantic dinner at a fancy restaurant.

Joey is chosen to be part of a group of students to paint a school mural, but when hers is defaced before the unveiling, Dawson offers words of encouragement while Pacey takes action and risks suspension when he goes in search of the culprit whom he suspects to be Matt. When Andie's PSAT scores rank among the best in the country, she feels tremendously guilt-ridden and gambles with everything she has worked for by telling Principal Green about the previously stolen PSAT test. Also, Pacey moves in with his brother, Doug, when their divorced sister and her kids move back into the Witter house and take over Pacey's room.

Joey relies on the support of Pacey and A.J. to rally the students in a major school protest against the school superintendent, Dr. Fielding, after he forces Principal Green to resign for expelling Matt Caulfield who destroyed Joey's mural after the guy's wealthy and powerful parents threaten the school board with a lawsuit. Meanwhile, Dawson and Gail both go back to their respective places in back and in front of the camera to produce a piece about the ongoing school protest which ruffles more than a few feathers of the school board hierarchy as well as Gail's old rival; a reporter named Sherry Eisle who "stole" Gail's old job back in Philadelphia and is now covering the story in her own self-serving and bias way.

Joey travels to Boston to visit A.J. where he is about to receive a critic writing award and meets his childhood friend, Morgan, whom Joey sees as a clone version of herself and her growing feelings for Pacey. Back in Capeside, to avoid suspension, Pacey becomes a mentor to a nine-year-old boy, named Buzz Thompson, and must contend with the kid whom is a little version of himself: a neglected and abused little boy - with a big attitude. Meanwhile, Dawson asks Mitch to help as a chef with the opening of Gail's restaurant which makes Gail angry as she wants nothing to do with her ex-husband.

Pacey hopes that an overnight camping trip by taking Dawson to their favorite childhood camping spot will help ease the pain when he prepares to tells Dawson about his romantic feelings for Joey. But their plans get interrupted when Buzz and two of his friends come along. When Dawson brings up memories about their loyal friendship, Pacey chickens out and decides not to tell Dawson. Meanwhile, Joey deals with the emotional fallout from her kiss with Pacey by spending a girls' night out with Jen and Andie. But to Jen's surprise, they stumble upon a 15th birthday party for Henry at the local roller skating rink that she was not invited to. Also, Jack clashes with his father when Ethan arrives at his house for a visit in which Ethan gets caught in the middle when Mr. McPhee bonds with him and not Jack.

Dawson invites Joey, Andie, and Pacey to spend Spring Break in the mountains of Vermont at his Aunt Gwen's home. But the trip is filled with tension as Joey and Pacey continue to battle about their feelings for each other and Andie becomes intrigued with the gang's childhood friend, Will, who is visiting. Back in Capeside, Jen, working as the hostess at Gail's new restaurant, Leery's Fresh Fish, becomes surprisingly territorial when a waitress, named Shelley, flirts with Henry who's now working there as a busboy. Also, Gail and Mitch question their current situation over being partners in the restaurant.

In this unusual episode that replays the same day's activities from three different perspectives: after Pacey unveils his new sailboat, named 'True Love', he and Joey vacillate on the ways to tell Dawson about their feelings for each other. But each time they decide to tell Dawson about them being romantically involved, they chicken out. But when both Pacey and Joey get together and decide to tell Dawson about them, Dawson's angry reaction is what they hoped they wouldn't get: Dawson reveals that he already knows when Jen had earlier that day told him about Joey and Pacey after assuming that they told Dawson. Meanwhile, Andie, who thought she was over Pacey enough to date, accepts a date with Capeside visitor Will, but their first date is ruined when she also learns about Joey and Pacey now a couple. Pacey also leaves the trouble-making Buzz with his brother Doug for the entire day as Andie deals with her feelings for will, Also Jen deals with Henry who wants to take their relationship to the next level.

As Capeside prepares for the Annual Spring Regatta boat race, Dawson and Pacey compete with each other for the winning trophy, only Joey is tired of feeling like the prize. Meanwhile, after many weeks of mixed messages, Gail makes the first move with Mitch. After Jen finally forgives Henry for his one-track mind, he gives Jen the most romantic night of her life with a moonlight picnic atop a building overlooking the bay.

Dawson, Joey and Andie prepare their own unique prom when they learn that the committee has scrutinized Jack's selected male date Ethan. Dawson, who has invited Joey to be his date, uses the special evening to try to win her back and make Pacey jealous. Andie persuades Pacey to be her escort, but her evening ends by her consoling him about his love life uncertainties. Also at the prom, Jen becomes outraged with Henry when he reveals he is leaving Capeside for the summer to attend football camp in Ohio, and Gail and Mitch celebrate their new found romance.

Pressured by two parties, Joey ultimately must choose between her love for Dawson and her new feelings for Pacey who's planning a summer getaway by sailing down the coast on his new boat, 'True Love.' Meanwhile, Grams talks about love and regret with Jen over the departed Henry, and encourages her, with Jack and Andie tagging along, for an all-night drive to Ohio so that Jen can see Henry one last time. They then take Jack to Boston to see Ethan who tells him that he has returned to his boyfriend. Mitch and Gail decide to get remarried and have the ceremony at their house with Dawson as the best man and Joey as the maid of honor. At the end, Dawson encourages Joey to make a move to follow her own path, and she runs off to join Pacey on his boat, leaving Dawson emotionally beaten and alone once again.